Posted
by
kdawson
on Tuesday June 16, 2009 @11:43PM
from the all-in-the-interpretation dept.

pdragon04 sends in the hardly surprising news that direct-to-consumer genetic testing isn't predicting diseases as well as they claim. "...[Francis] Collins, who played a central role in the Human Genome Project and is rumored to be the next head of the National Institutes of Health, announced at the Consumer Genetics Conference in Boston last week that he had had his genome analyzed [using a made-up name] by the big three of direct-to-consumer genetic testing: 23andMe, Navigenics, and DecodeMe. Collins said that sequence-wise, the tests 'appear to be highly accurate': there were almost no differences in the genotype information generated in the three different analyses. But there were significant differences in the numbers of genetic variations used to calculate disease risk, as well as the final risk score. ... For example, one company used 5 single nucleotide polymorphisms, or SNPs, to calculate risk for a particular disease, pronouncing Collins at low risk. Another used 10 SNPs, placing him at high risk, and the third used 15, concluding that he is at average risk."

Genotype doesn't completely determine phenotype but it does provide some input. Genotype with environmental effects and stochastic elements determines phenotype (broadly speaking, I'm oversimplifying slightly since how one classifies epigenetic factors is complicated). Moreover, genotype is a major factor. So if I know information about the genotype I can prepare a lot. If for example I have an allele that is connected to increase risk of colon cancer, I know to have colonoscopies more often. If I'm a female with a bad BRCA1 allele I know that I should have my breasts checked much more regularly. Etc. Your comment is sort of like saying "why should I learn about my family medical history if knowing about it can make my insurance premium go up?"

Your comment is sort of like saying "why should I learn about my family medical history if knowing about it can make my insurance premium go up?"

I don't think his comment was "sort of" anything. I think that was exactly what he was asking and I don't think you gave an adequate answer.

So let's see... you find out from your DNA screening not that you actually have any condition, but that you need more tests, more careful screening, regular check-ups, etc, because you're at high risk. Unfortunately, your insurance carrier catches wind of your DNA results and jacks up your premiums so now you can't afford health insurance, and ergo you can't afford to pay for any of these regular tests you've been told you need. And this is a stain on your health record that will last the rest of your life. Nice going.

I don't think you gave an adequate answer either, addressing only the financial side of an information gathering process which could very well lead to an extended and more fulfilling life. I think this is symptomatic of having a healthcare system which cares more about money than health.

You seem to be advocating a position whereby saving money is more important than knowing more about the specific body you have, and any potential problems you may have with it in the future.

I know its tempting to think of hypotheticals such as your cancer sufferer. Unfortunately in the current climate, it isn't a choice between "hmm, I know I'm prone to x disease let me take y preventative action" and "let me blow off knowing anything about my genetics." If I look at it from the position of your example, testing won't do any good whatsoever. He already has the condition. I might wish to have the option to swap money for having this information in the past. Fantasies are nice, sometimes very ni

Pragmatic only if you happen live in a country which has a health service who's main objective is to make money.

I live in a country which has a nationalised health service ( it's not great, and getting worse ), it's subsidised by taxes on things which generally cause inhealth ( cigarettes, Etc. ) and the very idea of gambling with information which could seriously affect the most important thing in your life is horrific, to me you're saying that you'd avoid the prostate check ( * ) because they might fin

I'm not an actuary for health care provider, so I don't know if they have access to family histories, targeted life expectancies or any of that. So, I can't answer that question. Although knowing the answer would be useful. Since, I agree that at least some of the information from genetic testing can be replicated/approximated from other information sources. And if such information is already used, there is less risk to genetic testing because of it.

And yet, as they overconsume, costs rise, calculations change and premiums rise. So what you don't pay directly to the care provider, you (more than) make up in periodic payments to your insurer. And that causes the consumer to think things like "I pay so much already, I may as well go consume even more health care".. it is a.. not optimal cycle.

It's not the colonoscopies they're looking for, it's the "I have the sniffles again this week and I NEED an antibiotic, doc! Don't worry, my insurance will cover it!"

That's where copayments and the point about covering only treatments that are both medically necessary and effective comes in. Treating a common cold with an antibiotic is neither, so if you wanted that antibiotic anyway (which your doctor should advise against, see the whole issue of resistances, plus you're messing up your digestive system

I went to the doctor to get a prescription for an asthma inhaler one morning (after a bad random attack with no rescue inhaler). She threw antibiotics (azithromycin?)at me as well, claiming I might have a mild upper respiratory infection.

The next time I went in (many months later), I was sick as shit, getting a respiratory infection.I had a busy week of work ahead of me, so I go in and ask for antibiotics. (Normally, I'd take a few sick days and tough it out and wait for the weekend.)The same doctor tells

Aside from how the health care is provided, I think the real question here is "how would the insurance companies get their hands on my DNA reports in the first place?" If you just plain got tested on your own dime, then that information should be between you and the testing company.

If you were tested as instructed by a doctor for an actual condition, that your insurance then had to pay for, you would expect that they could get their hands on it because they paid for it. Even then, it may be overreaching o

A) Healthy people overpay to cover the costs of the sick people or B) the company can charge you more when you're healthy to cover the costs of when you're sick.

or C) people get genetic tests under false names, find out they're going to be really sick, and then get the ultra-deluxe insurance they wouldn't have purchased otherwise, thus driving up rates for everybody, and forcing everybody to get genetic testing before deciding whether they want to pay for insurance.

Why would this affect insurance? This not a condition known before signing the insurance, as such the insurance has to accept the loss and carry the costs. The entire point of health insurance is to protect from new disease, which included new discovered diseases you could not have known you had when signing the insurance. If they just raises the premium for that, the might as well raise the premium if you get HIV from infected donor blood, or any other condition that is just raises the risk of other condit

Because private insurance companies are free to deny coverage to "unacceptable risks" or jack up your rates sky-high.

This not a condition known before signing the insurance, as such the insurance has to accept the loss and carry the costs.

That may be true, but don't even think of switching to a different insurance contract. You'll basically be locked into the one you have now (or locked out of getting any if you didn't have one before), and the insurance company is go

What kind of healthcare system would penalize someone for ensuring they are living the healthiest lifestyle possible?

One that is run for profit? In such a system, it doesn't matter how healthy your lifestyle is. All that matters is how large and calculable your risk is. If your genes say that you're an unacceptable risk, you can live as healthy as you want and sill not get any insurance (or a rate that pretty much says 'We don't want to insure you.').

The degree to which genotype determines phenotype lies in how you define phenotype. If you say phenotype is the risk of a disease, then your environment is going to play a huge role. If you say phenotype is the type and amount of protein your cells produce, then the two are practically interchangable (depending somewhat on gene regulation, but that's arguably genotype as well).

One of the more common misconceptions is that certain genes cause certain diseases. This isn't quite right. BRCA1, for example,

When my youngest was born, we were asked to partake in a study about childhood diabetes by giving a blood sample. Lots of diabetes in my family and she turned up to have a marker for it so she was asked to be part of the study. She never got diabetes but she did wind up having Celiac, a somewhat related issue. We ONLY found out about the Celiac because she was in the study... she was diagnosed via a blood test when she was (we thought) asymptomatic at the time. Celiac screening isn't (though should be) a r

In the United States, discrimination on the basis of genetic information or the requesting, requiring, or purchasing of genetic information by any health care plan is prohibited by the Genetic Information Nondiscrimination Act of 2008, passed by Congress in April 2008 and signed by President Bush the following month. Similarly, employers may not discriminate on the basis of genetic data, nor may they generally request nor require an employee to undergo genetic testing (there are a few very limited exceptions).

Basically, you can learn about your genome without worry that your insurance premiums will change, because with very limited exceptions, the insurers will never have access to it.

Try saying that to AIG and State Farm.StateFarm recently was in the news for rejecting coverage of someone whose DNA tests were known to it.Hitler would have loved this.It would have given the SS and Gestapo valid, legal reasons that were sought in this conference [wikipedia.org].

In the United States, discrimination on the basis of genetic information or the requesting, requiring, or purchasing of genetic information by any health care plan is prohibited by the Genetic Information Nondiscrimination Act of 2008

Which prohibits use of such information as the sole reason for discrimination. So if they see the information and deny you coverage because not only do you have bad genetics, but you're unattractive too, they're in the clear. It also does not appear to have criminal penalties

First, of all that's not accurate. Collins is pretty strongly against creationism in most of its forms, including classical young earth creationism and intelligent design. He is a variant of a theistic evolutionist with perhaps more of a notion of direct intervention by God than most theistic evolutionists. So describing him as you did is inaccurate.

Even if Collins views were not more moderate than you portray them, it wouldn't make his expertise any less. To use another example, I think that Noam Chomsky has a very strange ideas in his head about politics and how the media work. That doesn't mean I'm going to pay less attention to him when he talks about linguistics. Someone can have bad ideas in one area and still be an expert in another. Given his background, Collins clearly knows what he is talking about and is qualified to evaluate the products in question.

Religion isn't bad. Extremists are bad. Zealots are bad. Idiots are bad. Religion may bring about these things, or those with these may be attracted to religion, however that isn't the fault of the religion itself. If a country began to kill and oppress in the name of democracy would you say democracy was bad? If a man began to kidnap and rape people in the name of love would love be bad?

Two points:

1) Zealots have little power in the absence of a moderate base. The difference in influence between a Pat Robertson and a Jim Jones is quantitative, not qualitative.

2) Democracy and love are rather abstract concepts compared to the notion of a specific God who wants me to hate and persecute specific classes of people. That's the problem with the faith of someone like Francis Collins... his apologetics are all hand-wavy and woo-woo-driven, but the actual God he's evangelizing for has specific traits, specific likes and dislikes... and specific plans for humanity that simply are not compatible with the rational worldview we (should) demand of our scientists.

I like the Greek gods. They became intoxicated, had affairs...they were imperfect.

Jesus Christ was a pretty cool dude, but he was too perfect. Like Dostoevsky's Idiot, it was only a matter of time until he was thrown to the sidelines muttering and babbling to himself while the Grand Inquisitors siezed power.

Maybe Jesus was all happy hugs and kisses, but his dad, the guy that the Jesus worshipers believe is the real power, and the one with the ultimate say in all things, demands his followers be prepared to wage war, kill those that are different, rape, pillage, plunder, and murder their own children as human sacrifices.

Claims of Jesus's endorsement of piece and love doesn't give much comfort when he is only the SON of God. It's not like there would be any chance of him gaining the throne. It's documented

I tried that when I was young and found nothing. I felt much better after learning the truth. Life is much more pleasant living with my own, appropriate set of values, rather than the arbitrary BS that people tried to cram down my throat (granted, my values aren't much different from theirs, but now I don't have to put up with them). It also adds some comedic value when the odd extra-religious person looks at me funny and tries to avoid telling me that I'm going to hell for not believing.

God loves us enough not to end our existence despite the evils that we perpetrate or fall into. It may feel, some times, like everything would be better where we not to exist. But God's love is so great that he allows us to exist despite the pain of life.

I, personally, do not think I could look at anything and believe that there is a creator of all existence. My distance from your God is infinite because I do not believe He exists. I have no relationship with your God or any other god because, again, I do not believe that they exist.

I could go into detail exactly what I think about religion and its followers, but I will do my best to avoid insulting you. I respect your right to believe what you wish; please do the same for me.

Funny, I read the whole thing (including the 'God Bless' at the end) in Ned Flanders' voice. It makes it even more disturbing.;)

Sigs and religion aside, it's not surprising that this first wave of DIY genetic screening tests is somewhat iffy. It's a lot more complex than things like pregnancy tests, and they've only been around for a relatively short amount of time. Sorta like the difference between detecting a particular file on your computer vs. testing for a particular few bytes in that file being on

Francis Collins also believes that Jesus rode dinosaurs. [wordpress.com] He was once a respected scientist, but then he took a short step off a long intellectual pier. Why should I give his advice any consideration?

I'll see your "ad hominem [sic] fallacy" and raise you a "credibility of the witness."

In the ideal world of the philosophers, where all parties are equally able to evaluate all the arguments raised, attacks on character are indeed fallacious. 2+2=4, and it doesn't matter if the person telling you that is someone you like, someone you despise, or someone you don't know from Adam. But in the real world, nobody knows everything. Most of the time, most p

I'll see your "ad hominem [sic] fallacy" and raise you a "credibility of the witness."

If you don't know what "sic" means, don't use it.

Also, the expert's beliefs in some other field do not affect his skill in his specialty. A fantastic chef might have appalling taste in wine, but that won't stop me from eating at his restaurant, because all I care about is the skill in question.

[sigh] I know exactly what "sic" means, and if you carefully read my post and the post I responded to, you'll see why I used it.

Your example of the chef doesn't really hold up. You're the only one qualified to decide if you like the way his food tastes; there are no issues of fact to debate. A closer analogy would be one of food safety -- no matter how tasty the food that comes out of the kitchen, would you be comfortable eating at a restaurant where the head chef had gone on record stating that he thoug

Sounds like there's room in the market for just the risk analysis. No reason to have the dirty work done three times - just sequence once and get a whole range of opinions, or focus on certain areas for detailed analysis. maybe this already exists.

To judge from the complaints that frequently get posted to the GENEALOGY-DNA mailing list, even the experienced big-name DNA corps screw up on even testing a few dozen STRs. The chances of fouling up somewhere along the entire genome seems extremely high. Thus, redundant testing seems a really good idea - at least until they improve their methods.

On the other hand, there probably IS a huge market for risk analysis. The DNA analysis market is pretty much glutted, but there's not much out there for DNA analysis for the average person at the moment.

It is worth bearing in mind that the sorts of studies done might not pick up all of the secondary genetic data needed - markers whose presence doesn't alter the probability of a condition UNLESS the primary marker is also present. Simply doing a gigantic "diff" isn't going to pick those up, as their presence isn't always important.

Then, there are conditions with multiple genetic triggers. Chronic fatigue has seven, according to a BBC report a while back, each of which produces a different condition with essentially identical symptoms but which respond to different treatments. (Unless there's genetic overlap, I would assume this means there are 5040 potential conditions that could be produced from these markers.)

Then, on top of all that, some conditions may occur but be too mild to notice. There are claims that autism is far more common than currently thought and certainly, the UK diagnoses it twice as often as the US (implying that either closer examination DOES yield more positives, or that us British are just strange). There's also a claim that many, if not most, people have some degree of synaesthesia. But is it useful to know that there's a very high risk of being normal?

(Ok, ok, Slashdotters might want to know if there's a genetic danger of becoming normal, but ASIDE from that...)

It would seem to me that conditions such as autism and synaesthesia follow something close to a Poisson distribution, with the vast bulk of people at close to no effect. Even if they're absolutely guaranteed the effect, they'll never notice.

Unless studies into risk go far, far beyond the horribly basic and naive results you get at the moment, the results are useless. And that kind of massive data-crunching analysis is something that Beowulf clusters and BOINC clients are going to be very good at......provided an answer even exists. If the severity isn't present in the DNA, then the risk is useless.

I RTFA and fail to see what the pros/cons of each service is, and which one he recommends.

That's because he can't recommend any on the basis of the results or methodology of the testing.

SNPs can be a useful tool, but because (by definition) they are single nucleotides, you need a lot of them to be able to validate a pattern. From the submission, he mentions 3 labs using 5, 10 and 15 SNPs and claiming to be able to draw inferrences from these. My understanding (FWIW) is that a mere 5 polymorphisms are not

Problem is, he doesn't specify which labs use more SNPs or "more useful" SNPs (which as you mentioned, should provide better/more accurate results).

The point of experiments and tests should be to draw some conclusion (even if the conclusion is that all fail) but clearly some services are performing better than others and are turning out more accurate. Why does he not state, in his professional and unbiased opinion, which one is better?

Problem is, he doesn't specify which labs use more SNPs or
"more useful" SNPs (which as you mentioned, should provide better/more
accurate results).

Primarily because it's not known yet for a large number of
diseases.

The point of experiments and tests should be to draw some
conclusion (even if the conclusion is that all fail) but clearly some
services are performing better than others and are turning out more
accurate. Why does he not state, in his professional and unbiased
opinion, which one is better?

Clearly the statistical analyses' are wrong for at least two of those companies. The prior probability of risk for a given disease is 'average', and if you don't test enough polymorphisms or if the correlations are weak then it remains average. Trouble is you can't make a business case on selling such weak information, so there's an incentive to spice up the summary info they provide.

The practice of using different numbers of gene sequences is common: the same thing happens if you get an HIV test, or an HPV test, or FLU, or whatever. In that case though, the FDA regulates it to prove that the result is clinically valid. I'm not sure what involvement the FDA has in this.

One item in the article that surprised me: the companies aren't offering information to their clients about diseases they are carriers for. For instance, it would add value to their service if clients knew they carried the gene for cystic fibrosis (a common genetic test).

It's either a huge oversight by the 'big three', or they think that their clients are so focused on themselves as to not really care about what diseases their children could inherit.

One item in the article that surprised me: the companies aren't offering information to their clients about diseases they are carriers for. For instance, it would add value to their service if clients knew they carried the gene for cystic fibrosis (a common genetic test).

That's kind of odd, because at least 23andme (haven't checked the others) seems to offer information on whether someone is a cystic fibrosis carrier:

Cystic Fibrosis is one of the conditions that 23andMe analyzes. Our service includes the following information:

* Whether or not you are a carrier for the Delta F508 mutation linked to cystic fibrosis.* Information on i3000001, a marker that influences your carrier status for Cystic Fibrosis.* Background information on Cystic Fibrosis and a list of counselors, links and support groups in your area.

I began performing SNP analysis on genomic DNA for schizophrenic patients back in 2002 in the new Pharmacogenoics group of a large Pharmaceutical company. Our goal was to correlate drug effect to the genetic background of the individual. If we could establish a relationship we could potentially get a few failed drugs to perform "better" when used in patients genetically predisposed for a positive effect and get them into the market.

All of our results required TEAMS of statisticians to figure out if the

The defense lawyers used widely varying statistical numbers from scientific experts to create doubt as to whether OJ Simpson's genes matched blood found at the crime scene. This was one piece of doubt among several others in the case before a jury eager to find any reasonable doubt to acquit.